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--- dev:regtesting [2020/04/06 17:59] – make can also use options listed in do_regtest xinwu
+++ dev:regtesting [2023/10/19 14:03] (current) – Update flags krack
@@ Line 11: / Line 11: @@
 ===== How does it work? =====
-The regression test suite is run using the [[src>tools/regtesting/do_regtest | do_regtest]] script.
+The regression test suite is run using the [[src>tests/do_regtest.py | do_regtest]] script.
 It performs the following tasks:
    * performs a realclean build of the source
@@ Line 23: / Line 23: @@
 ==== Step 0: make based testing ====
-  * If you are able to build and run cp2k on the local machine the easiest way is to start the regtesting by running ''make ARCH=... VERSION=... test''. The options listed in Step 2 can also be specified with ''make'' via ''TESTOPTS+=<options>'', e.g. ''TESTOPTS+="-mpiranks 4 -ompthreads 4"'' requires 4 MPI ranks and 4 OpenMP threads for each MPI rank.
+  * If you are able to build and run cp2k on the local machine the easiest way is to start the regtesting by running ''make ARCH=... VERSION=... test''. The options listed in Step 2 can also be specified with ''make'' via ''TESTOPTS=<options>'', e.g. ''TESTOPTS+="--mpiranks 4 --ompthreads 4"'' requires 4 MPI ranks and 4 OpenMP threads for each MPI rank.
   * Be careful about the value of ''-j'' parameter you will use; running too many tests in parallel can cause tests to fail due to lack of system and/or GPU memory.
   * If this fails (e.g. on batch systems), continue with Step 1 else go to interpretation.
@@ Line 34: / Line 34: @@
 ==== Step 2: Running ====
 <code>
-$ tools/regtesting/do_regtest --help
+$ tests/do_regtest.py -h
-Usage: do_regtest [OPTION]
+usage: do_regtest.py [-h] [--mpiranks MPIRANKS] [--ompthreads OMPTHREADS]
-Run the CP2K regression test suite
+                     [--maxtasks MAXTASKS] [--num_gpus NUM_GPUS]
-Example: do_regtest -c my_regtest.conf
+                     [--timeout TIMEOUT] [--maxerrors MAXERRORS]
+                     [--mpiexec MPIEXEC] [--smoketest] [--valgrind]
+                     [--keepalive] [--flagslow] [--debug]
+                     [--restrictdir RESTRICTDIR] [--skipdir SKIPDIR]
+                     [--workbasedir WORKBASEDIR] arch version
-General:
+Runs CP2K regression test suite.
-  -h, -help, --help         print this help screen.
-  -c, -config FILE          read any of the following configuration switches from FILE.
-  -cp2kdir PATH             location of cp2k source tree relative to current working directory.
-  -dirout PATH              root path of output folder (default: current working directory).
-  -mpiexec EXE              name of the executable to run mpi-ranks. Default: mpiexec.
-Build:
+positional arguments:
-  -version VERSION          VERSION passed to make. Default: sopt.
+  arch
-  -arch ARCH                ARCH passed to make. Default: Linux-x86-64-gfortran.
+  version
-  -quick                    rebuild if needed, but without realclean. Default: off.
-  -nobuild                  do not build cp2k, rely on user's build. Default: off.
-Runtime:
+options:
-  -mpiranks NRANKS          number of mpi-ranks. Default: 2 for parallel versions, 1 for serial.
+  -h, --help            show this help message and exit
-  -ompthreads NTHREADS      number of OpenMP threads. Default: 2 for smp versions otherwise 1.
+  --mpiranks MPIRANKS
-  -maxtasks NPROCS          total number of processor to use. Default: `nproc`.
+  --ompthreads OMPTHREADS
-  -maxbuildtasks NPROCS     total number of processor to use for compilation. Default taken from -maxtasks.
+  --maxtasks MAXTASKS
-  -jobmaxtime SECONDS       maximum execution time of a single test. Default 600.
+  --num_gpus NUM_GPUS
-  -farming                  test via a single farming run (only for parallel cp2k).
+  --timeout TIMEOUT
+  --maxerrors MAXERRORS
-Testing:
+  --mpiexec MPIEXEC
-  -noreset                  do not reset the reference outputs. Default: off.
+  --smoketest           Runs only the first test of each directory.
-  -shard ISHARD NSHARDS     do sharding: Divide the test dirs into NSHARD subsets and only run the ISHARD-th set.
+  --valgrind            Runs tests under Valgrind memcheck. Best used together with --keepalive.
-  -skiptest                 do not run test, only build. Default: off.
+  --keepalive           Use a persistent cp2k-shell process to reduce startup time.
-  -skipunittest             do not run unit tests. Default: off.
+  --flagslow            Flag slow tests in the final summary and status report.
-  -skipdir TESTDIR          do not run tests in TESTDIR. This switch can repeated.
+  --debug
-  -restrictdir TESTDIR      run only tests in TESTDIR. This switch can repeated.
+  --restrictdir RESTRICTDIR
-  -retest                   run only tests in directories, which had failing tests in previous run.
+  --skipdir SKIPDIR
+  --workbasedir WORKBASEDIR
-Exit codes:
-   clean exit with testing
-   problem with realclean
-   build errors
-   problem with retest option - no TEST directory with latest test results found
-   problem with retest option - no error summary exists in the last TEST directory
-   reference directory is locked
-   ctrl-C (SIGINT) and various other signals trapped
-For more information visit: <http://cp2k.org/dev:regtesting>
 </code>
@@ Line 102: / Line 89: @@
 | ''TEST_TYPES''       | this file allows you to create a new test type. I.e. to specify for which words should be grepped and what field should be used in the numerical comparison. |
+===== Run with sbatch =====
+The ''%%do_regtest%%'' script in ''%%tools/regtesting%%'' is often run from ''%%make VERSION=... ARCH=... test%%'' where it sets up everything just nicely. On a cluster you usually do want to separate the steps and invoke ''%%do_regtest%%'' manually.
+What you need:
+  * ''%%sbatch%%'' template script
+  * a CP2K source tree with a built CP2K
+==== Instructions ====
+The way the regtest script works is that it goes through all the directories (for example ''%%tests/QS/regtest-admm-1/%%'') and launches all tests in that directory. After each directories tests are started it checks whether the number of maximum tasks is reached, if not it also spawns the tests from the next directory. If the maximum number of tasks to run has been reached it waits until enough of them have finished to spawn tests from the next directory. Since the tests are usually rather short this procedure seldomly causes oversubscription.
+Also, ''%%srun%%'' should simply wait until nodes are free should there be no more free nodes available within the given allocation. Hence, the more nodes (or total number of tasks) you allocate for the ''%%sbatch%%'' the more tests can run in parallel. But we have to make sure ''%%do_regtest%%'' knows about that number by setting ''%%-maxtasks ${SLURM_NTASKS}%%'', ''%%SLURM_NTASKS%%'' is automatically set by ''%%sbatch%%'' to the number of tasks you specified either when running ''%%sbatch%%'' or in the preamble of the ''%%sbatch%%'' script.
+Append the following to your ''%%sbatch%%'' template and at least adapt the value for ''%%CP2K_BASE_DIR%%'' and possibly also the ''%%CP2K_TEST_DIR%%'':
+<code bash>
+CP2K_BASE_DIR="/PATH/TO/YOUR/CP2K/SOURCE/TREE"
+CP2K_TEST_DIR="${SCRATCH}/cp2k_regtesting"
+# CP2K_REGTEST_SCRIPT_DIR=""  # only set if needed (see below)
+CP2K_ARCH="local"
+CP2K_VERSION="psmp"
+# the following is the default, adjust if you want to run single tests with more than 2 ranks/tasks
+NTASKS_SINGLE_TEST=2
+NNODES_SINGLE_TEST=1  # otherwise srun will distribute the 2 tasks over 2 nodes
+SRUN_CMD="srun --cpu-bind=verbose,cores"
+# the following should be sufficiently generic:
+mkdir -p "${CP2K_TEST_DIR}"
+cd "${CP2K_TEST_DIR}"
+cp2k_rel_dir=$(realpath --relative-to="${CP2K_TEST_DIR}" "${CP2K_BASE_DIR}")
+# srun does not like `-np`, override the complete command instead:
+export cp2k_run_prefix="${SRUN_CMD} -N ${NNODES_SINGLE_TEST} -n ${NTASKS_SINGLE_TEST}"
+"${CP2K_REGEST_SCRIPT_DIR:-${CP2K_BASE_DIR}/tools/regtesting}/do_regtest" \
+  -arch "${CP2K_ARCH}" \
+  -version "${CP2K_VERSION}" \
+  -nobuild \
+  -mpiranks ${NTASKS_SINGLE_TEST} \
+  -ompthreads ${OMP_NUM_THREADS} \
+  -maxtasks ${SLURM_NTASKS} \
+  -cp2kdir "${cp2k_rel_dir}" \
+  |& tee "${CP2K_TEST_DIR}/${CP2K_ARCH}.${CP2K_VERSION}.log"
+# the above will output both to the slurm-*.out as well as a log file,
+# if you want only the log file replace the `|& tee` with a `>&`.
+# More options:
+# -farming   ... enable farming mode, see below
+# -retest    ... only do tests which failed in a previous run
+</code>
+A complete ''%%sbatch%%'' script to run the regtests on CSCS’ Alps (Eiger) could look as follows:
+<code bash>
+#!/bin/bash -l
+#SBATCH --time=01:00:00
+#SBATCH --nodes=4
+#SBATCH --ntasks-per-node=128
+#SBATCH --cpus-per-task=2
+#SBATCH --ntasks-per-core=1
+# More SBATCH options:
+# If you need 512GB memory nodes (otherwise only 256GB guaranteed):
+#    #SBATCH --mem=497G
+# To run on the debug queue (max 10 nodes, 30 min):
+#    #SBATCH--partition=debug
+set -o errexit
+set -o nounset
+set -o pipefail
+export MPICH_OFI_STARTUP_CONNECT=1
+export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
+export OMP_PROC_BIND=close
+export OMP_PLACES=cores
+source "${MODULESHOME}/init/bash"
+module load cpeGNU
+module load \
+    cray-fftw \
+    ELPA/2020.11.001 \
+    libxsmm/1.16.1 \
+    libxc/5.1.3 \
+    Libint-CP2K/2.6.0 \
+    gcc/10.2.0
+# Let the user see the currently loaded modules in the slurm log for completeness:
+module list
+CP2K_BASE_DIR="/users/timuel/work/cp2k"
+CP2K_TEST_DIR="${SCRATCH}/cp2k_regtesting"
+CP2K_ARCH="Eiger-gfortran"
+CP2K_VERSION="psmp"
+NTASKS_SINGLE_TEST=2
+NNODES_SINGLE_TEST=1
+SRUN_CMD="srun --cpu-bind=verbose,cores"
+# to run tests across nodes (to check for communication effects), use:
+# NNODES_SINGLE_TEST=4
+# SRUN_CMD="srun --cpu-bind=verbose,cores --ntasks-per-node 2"
+# the following should be sufficiently generic:
+mkdir -p "${CP2K_TEST_DIR}"
+cd "${CP2K_TEST_DIR}"
+cp2k_rel_dir=$(realpath --relative-to="${CP2K_TEST_DIR}" "${CP2K_BASE_DIR}")
+# srun does not like `-np`, override the complete command instead:
+export cp2k_run_prefix="${SRUN_CMD} -N ${NNODES_SINGLE_TEST} -n ${NTASKS_SINGLE_TEST}"
+"${CP2K_REGEST_SCRIPT_DIR:-${CP2K_BASE_DIR}/tools/regtesting}/do_regtest" \
+  -arch "${CP2K_ARCH}" \
+  -version "${CP2K_VERSION}" \
+  -nobuild \
+  -mpiranks ${NTASKS_SINGLE_TEST} \
+  -ompthreads ${OMP_NUM_THREADS} \
+  -maxtasks ${SLURM_NTASKS} \
+  -cp2kdir "${cp2k_rel_dir}" \
+ |& tee "${CP2K_TEST_DIR}/${CP2K_ARCH}.${CP2K_VERSION}.log"
+</code>
+==== Test parallelization via Farming ====
+Since the startup time of ''%%srun%%'' can be significant (the ''%%--bcast%%'' argument for ''%%srun%%'' might help if the binary is statically linked as does putting the CP2K directory on to a scratch volume) there is the option to use CP2Ks //Farming// mode to run all tests within one ''%%srun%%'' and one CP2K instance. This mode is directly supported by ''%%do_regtest%%'' which then dynamically creates the required CP2K input file. The drawback is that if one regtest triggers a ''%%CPABORT%%'' (or another signal) the rest of the tests will never run.
+Simply add the option ''%%-farming%%'' to the list of options for the ''%%do_regtest%%'' call to enable this.
+==== Minimal directory setup ====
+If you want to test a precompiled executable there is a minimal directory layout you have to reproduce to run the regtest:
+  * ''%%cp2k-prebuilt/exe/prebuilt/*.psmp%%'' … directory with all the executables
+  * ''%%cp2k-prebuilt/tests%%'' … directory containing the tests (can NOT be a symlink)
+  * ''%%cp2k-prebuilt/data%%'' … containing CP2Ks data
+An example if your HPC center uses EasyBuild to provide the CP2K package:
+<code>
+cp2k-prebuilt
+├── data -> /apps/eiger/UES/jenkins/1.4.0/software/CP2K/8.1-cpeGNU-21.04/data
+├── exe
+│   └── prebuilt -> /apps/eiger/UES/jenkins/1.4.0/software/CP2K/8.1-cpeGNU-21.04/bin
+└── tests
+</code>
+and then update the variables as follows:
+<code bash>
+CP2K_BASE_DIR="/PATH/TO/THE/MINIMAL/DIR/cp2k-prebuilt"
+CP2K_TEST_DIR="${SCRATCH}/cp2k_regtesting"
+CP2K_REGTEST_SCRIPT_DIR="/PATH/TO/A/FULL/CP2K/DIR/tools/regtesting"
+CP2K_ARCH="prebuilt"
+CP2K_VERSION="psmp"
+</code>
+**Note**: if the ''%%tools/regtesting%%'' is not in that minimal directory tree as shown above you may get an error about the ''%%timings.py%%'' not found and there will be no timings. If you need those you should link/copy the regtesting scripts into ''%%tools/regtest%%'' of that minimal directory tree, at which you point you can leave the ''%%CP2K_REGTEST_SCRIPT_DIR%%'' variable undefined again.